/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.masked /home/seqanal//RepeatMasker20020713/Libraries/is.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/identity.matrix -minmatch 15 -minscore 17 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181603
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ...1.008 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.654 Mbytes in 4 blocks
Complementing ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.654 Mbytes in 4 blocks
Allocating align_entries ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.379 Mbytes in 4 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 1.512 Mbytes; currently free: 0.379 Mbytes in 4 blocks
4.536 Mbytes allocated -- total 6.048 Mbytes
Finding words ...
 0  735341
 10  311103
 20  1127
 30  408
 40  276
 50  101
 60  62
 70  44
 80  24
 90  34
 100  28
 110  8
 120  2
 130  11
 140  2
 150  2
 160  1
 860  2
min no. words: 0 at 22
max no. words: 859 at 0
avg no. words: 0.02.520 Mbytes allocated -- total 8.568 Mbytes
1.008 Mbytes allocated -- total 9.576 Mbytes
 Done
Total space allocated: 9.576 Mbytes; currently free: 1.445 Mbytes in 7 blocks
550000 words; after pruning: 549972
Sorting words ... Done

15  503032
Finding subject matches ...1.008 Mbytes allocated -- total 10.584 Mbytes
3.024 Mbytes allocated -- total 13.608 Mbytes
3.528 Mbytes allocated -- total 17.136 Mbytes
 Done
Total space allocated: 17.136 Mbytes; currently free: 4.879 Mbytes in 11 blocks
# pass words: 6, #fail words: 8
Quickalign: 1 successes, 0 failures
8 SWAT alignments performed. 0 pairs have score >= 17
Making reversed pairs ... Done
Total space allocated: 17.136 Mbytes; currently free: 11.824 Mbytes in 13 blocks
Printing matches ...  Done
Total space allocated: 17.136 Mbytes; currently free: 11.824 Mbytes in 14 blocks
Checking pairs ... Done
Total space allocated: 17.136 Mbytes; currently free: 11.824 Mbytes in 13 blocks
Total space allocated: 17.136 Mbytes; currently free: 11.824 Mbytes in 13 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181603
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  970288
 10  78128
 20  130
 30  18
 40  8
 50  1
 80  1
 140  2
min no. words: 0 at 4
max no. words: 139 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  78288
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
.... Done
Total space allocated: 7.056 Mbytes; currently free: 1.272 Mbytes in 7 blocks
# pass words: 13929, #fail words: 0
Quickalign: 78 successes, 19 failures
4940 SWAT alignments performed. 97 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.932 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.685 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.685 Mbytes in 7 blocks
Total space allocated: 7.056 Mbytes; currently free: 5.685 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1231, in 97 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p51g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181603
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.281 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.281 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  970586
 10  77838
 20  133
 30  8
 40  9
 140  2
min no. words: 0 at 4
max no. words: 137 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.613 Mbytes in 4 blocks
92744 words; after pruning: 92606
Sorting words ... Done

10  77990
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.
descrip_buffer expanded1.008 Mbytes allocated -- total 7.560 Mbytes
 Done
Total space allocated: 7.560 Mbytes; currently free: 1.789 Mbytes in 9 blocks
# pass words: 3681, #fail words: 13142
Quickalign: 258 successes, 83 failures
1996 SWAT alignments performed. 337 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.426 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.179 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.180 Mbytes in 10 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.180 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 16148, in 337 lists, size: 0.016 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p51g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181604
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.338 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.338 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.297 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.297 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  975470
 10  73066
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.180 Mbytes in 3 blocks
82044 words; after pruning: 81602
Sorting words ... Done

10  73106
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.932 Mbytes in 9 blocks
# pass words: 598, #fail words: 3495
Quickalign: 2 successes, 0 failures
498 SWAT alignments performed. 2 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.534 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.310 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.310 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.310 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 114, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p51g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181604
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.338 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.338 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.297 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.297 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  975501
 10  73035
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.180 Mbytes in 3 blocks
82044 words; after pruning: 81558
Sorting words ... Done

11  78018
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
..0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.925 Mbytes in 8 blocks
# pass words: 2825, #fail words: 5969
Quickalign: 58 successes, 31 failures
2852 SWAT alignments performed. 87 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.522 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.297 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.297 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.297 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 4713, in 87 lists, size: 0.005 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p51g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181607
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976761
 10  71775
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.190 Mbytes in 3 blocks
80658 words; after pruning: 80128
Sorting words ... Done

11  76638
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
 Done
Total space allocated: 6.048 Mbytes; currently free: 0.445 Mbytes in 7 blocks
# pass words: 465, #fail words: 1339
Quickalign: 7 successes, 20 failures
498 SWAT alignments performed. 27 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.038 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.817 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.817 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.817 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2010, in 27 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p51g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181607
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976727
 10  71809
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.189 Mbytes in 3 blocks
80658 words; after pruning: 80176
Sorting words ... Done

10  71849
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.952 Mbytes in 10 blocks
# pass words: 587, #fail words: 3486
Quickalign: 6 successes, 7 failures
509 SWAT alignments performed. 11 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.546 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.324 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.325 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.325 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 769, in 11 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181608
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  203180
 10  58922
 20  18
 30  10
 40  12
 50  2
min no. words: 0 at 5
max no. words: 44 at 62668
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.313 Mbytes in 3 blocks
80658 words; after pruning: 79720
Sorting words ... Done

9  58964
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes

descrip_buffer expanded.0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 1.072 Mbytes in 10 blocks
# pass words: 1650, #fail words: 5948
Quickalign: 13 successes, 2 failures
1617 SWAT alignments performed. 14 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.519 Mbytes in 10 blocks
Printing matches ... 0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.802 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.802 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.802 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 399, in 14 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181608
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977285
 10  71251
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.193 Mbytes in 3 blocks
80658 words; after pruning: 79400
Sorting words ... Done

10  71291
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded......... Done
Total space allocated: 6.048 Mbytes; currently free: 0.444 Mbytes in 9 blocks
# pass words: 10935, #fail words: 21882
Quickalign: 32 successes, 12 failures
10790 SWAT alignments performed. 40 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.034 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.812 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.813 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.813 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1218, in 40 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181613
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980190
 10  68346
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.210 Mbytes in 3 blocks
80658 words; after pruning: 75990
Sorting words ... Done

10  68386
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
....
descrip_buffer expanded. Done
Total space allocated: 6.048 Mbytes; currently free: 0.461 Mbytes in 9 blocks
# pass words: 5564, #fail words: 12711
Quickalign: 18 successes, 38 failures
5469 SWAT alignments performed. 48 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.031 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.809 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.810 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.810 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 3812, in 48 lists, size: 0.004 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p51g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181617
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  30905
 10  34517
 20  92
 30  6
 40  11
 50  4
 80  1
min no. words: 0 at 4
max no. words: 80 at 13107
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.623 Mbytes in 4 blocks
80658 words; after pruning: 74160
Sorting words ... Done

8  34631
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
.. Done
Total space allocated: 2.520 Mbytes; currently free: 0.874 Mbytes in 7 blocks
# pass words: 3753, #fail words: 6770
Quickalign: 19 successes, 23 failures
2949 SWAT alignments performed. 33 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.505 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.795 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.796 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.796 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1606, in 33 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p51g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181619
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  32754
 10  32682
 20  78
 30  6
 40  11
 50  4
 80  1
min no. words: 0 at 4
max no. words: 80 at 13107
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.660 Mbytes in 4 blocks
80658 words; after pruning: 66918
Sorting words ... Done

8  32782
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.682 Mbytes in 5 blocks
# pass words: 268, #fail words: 312
Quickalign: 0 successes, 0 failures
263 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.279 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.279 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.279 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.279 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181619
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  988301
 10  60235
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.257 Mbytes in 3 blocks
80658 words; after pruning: 66620
Sorting words ... Done

11  63764
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.... Done
Total space allocated: 6.048 Mbytes; currently free: 0.781 Mbytes in 6 blocks
# pass words: 4244, #fail words: 8169
Quickalign: 0 successes, 0 failures
4160 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.309 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.309 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.309 Mbytes in 5 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.309 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p49g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181628
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  211082
 10  51020
 20  18
 30  10
 40  12
 50  2
min no. words: 0 at 4
max no. words: 44 at 62668
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.378 Mbytes in 3 blocks
80658 words; after pruning: 66816
Sorting words ... Done

9  51062
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
.0.504 Mbytes allocated -- total 3.024 Mbytes
.... Done
Total space allocated: 3.024 Mbytes; currently free: 0.629 Mbytes in 7 blocks
# pass words: 5859, #fail words: 15560
Quickalign: 0 successes, 6 failures
5433 SWAT alignments performed. 6 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.011 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.798 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.798 Mbytes in 8 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.798 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 219, in 6 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181633
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  211096
 10  51022
 20  12
 30  10
 40  4
min no. words: 0 at 4
max no. words: 32 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.380 Mbytes in 3 blocks
80658 words; after pruning: 66432
Sorting words ... Done

9  51048
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
 Done
Total space allocated: 3.024 Mbytes; currently free: 0.638 Mbytes in 7 blocks
# pass words: 15293, #fail words: 0
Quickalign: 7 successes, 0 failures
365 SWAT alignments performed. 7 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.019 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.806 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.806 Mbytes in 8 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.806 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 174, in 7 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181633
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  32827
 10  32645
 20  64
min no. words: 0 at 4
max no. words: 18 at 21781
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.666 Mbytes in 4 blocks
80658 words; after pruning: 65686
Sorting words ... Done

8  32709
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
. Done
Total space allocated: 2.520 Mbytes; currently free: 0.925 Mbytes in 7 blocks
# pass words: 40820, #fail words: 0
Quickalign: 6 successes, 0 failures
1174 SWAT alignments performed. 6 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.515 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.806 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.806 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.806 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 84, in 6 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181633
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Finding words ...
 10  78
 20  96
 30  80
 40  120
 50  90
 60  92
 70  76
 80  78
 90  62
 100  48
 110  46
 120  32
 130  28
 140  22
 150  22
 160  14
 170  14
 180  12
 190  2
 200  6
 210  4
 220  2
min no. words: 3 at 102
max no. words: 214 at 330
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.420 Mbytes in 3 blocks
80658 words; after pruning: 65622
Sorting words ... Done

5  1024
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
.... Done
Total space allocated: 1.512 Mbytes; currently free: 0.441 Mbytes in 4 blocks
# pass words: 24053, #fail words: 0
Quickalign: 0 successes, 0 failures
4284 SWAT alignments performed. 0 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.773 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 1.512 Mbytes; currently free: 0.773 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.773 Mbytes in 4 blocks
Total space allocated: 1.512 Mbytes; currently free: 0.773 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181633
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  967001
 10  81529
 20  44
 80  2
min no. words: 0 at 5
max no. words: 80 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  81575
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.... Done
Total space allocated: 6.552 Mbytes; currently free: 0.768 Mbytes in 6 blocks
# pass words: 7658, #fail words: 0
Quickalign: 119 successes, 0 failures
4268 SWAT alignments performed. 119 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.428 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.180 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.181 Mbytes in 6 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.181 Mbytes in 6 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 519, in 119 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p43g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181633
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  967171
 10  81361
 20  42
 80  2
min no. words: 0 at 5
max no. words: 80 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.608 Mbytes in 4 blocks
93398 words; after pruning: 93300
Sorting words ... Done

10  81405
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.
descrip_buffer expanded1.008 Mbytes allocated -- total 7.560 Mbytes
 Done
Total space allocated: 7.560 Mbytes; currently free: 1.779 Mbytes in 9 blocks
# pass words: 3068, #fail words: 9857
Quickalign: 171 successes, 105 failures
1774 SWAT alignments performed. 264 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.424 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.176 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.177 Mbytes in 11 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.177 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 13226, in 264 lists, size: 0.013 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p43g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181634
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.337 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.337 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.295 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.295 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  972747
 10  75827
 30  2
min no. words: 0 at 1
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.170 Mbytes in 3 blocks
83570 words; after pruning: 83150
Sorting words ... Done

10  75829
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.910 Mbytes in 10 blocks
# pass words: 450, #fail words: 2918
Quickalign: 0 successes, 2 failures
385 SWAT alignments performed. 2 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.520 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.293 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.293 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.293 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 164, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p43g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181634
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.337 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.337 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.296 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.296 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  973226
 10  75348
 30  2
min no. words: 0 at 1
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.174 Mbytes in 3 blocks
82966 words; after pruning: 82504
Sorting words ... Done

11  80276
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
.. Done
Total space allocated: 6.552 Mbytes; currently free: 0.919 Mbytes in 8 blocks
# pass words: 2435, #fail words: 6018
Quickalign: 26 successes, 24 failures
2457 SWAT alignments performed. 50 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.523 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.296 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.297 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.297 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2537, in 50 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p43g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181637
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.338 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.338 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.297 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.297 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  974092
 10  74484
min no. words: 0 at 1
max no. words: 9 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.181 Mbytes in 3 blocks
81994 words; after pruning: 81488
Sorting words ... Done

11  79312
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.924 Mbytes in 9 blocks
# pass words: 1059, #fail words: 1644
Quickalign: 12 successes, 65 failures
660 SWAT alignments performed. 77 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.511 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.287 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.287 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.287 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 13977, in 77 lists, size: 0.014 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p43g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181637
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976498
 10  72078
min no. words: 0 at 1
max no. words: 7 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.200 Mbytes in 3 blocks
79076 words; after pruning: 78596
Sorting words ... Done

10  72078
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.733 Mbytes in 7 blocks
# pass words: 282, #fail words: 1549
Quickalign: 0 successes, 0 failures
277 SWAT alignments performed. 0 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 7 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 7 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p43g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181638
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  202474
 10  59668
 20  2
min no. words: 0 at 1
max no. words: 11 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.321 Mbytes in 3 blocks
79076 words; after pruning: 78644
Sorting words ... Done

9  59670
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes

descrip_buffer expanded0.504 Mbytes allocated -- total 3.528 Mbytes
. Done
Total space allocated: 3.528 Mbytes; currently free: 1.095 Mbytes in 10 blocks
# pass words: 1124, #fail words: 3903
Quickalign: 23 successes, 0 failures
1086 SWAT alignments performed. 20 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.536 Mbytes in 9 blocks
Printing matches ... 0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 11 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 439, in 20 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p43g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181638
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976716
 10  71860
min no. words: 0 at 1
max no. words: 7 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.201 Mbytes in 3 blocks
79076 words; after pruning: 78332
Sorting words ... Done

10  71860
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded......... Done
Total space allocated: 6.048 Mbytes; currently free: 0.463 Mbytes in 9 blocks
# pass words: 10229, #fail words: 21727
Quickalign: 3 successes, 5 failures
10060 SWAT alignments performed. 8 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.049 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.831 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.831 Mbytes in 10 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.831 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 352, in 8 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p43g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181643
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977612
 10  70964
min no. words: 0 at 1
max no. words: 7 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.207 Mbytes in 3 blocks
79076 words; after pruning: 77176
Sorting words ... Done

10  70964
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
..0.504 Mbytes allocated -- total 6.552 Mbytes
..
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 0.972 Mbytes in 9 blocks
# pass words: 5707, #fail words: 12721
Quickalign: 1 successes, 42 failures
5492 SWAT alignments performed. 43 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.542 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.324 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.324 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.324 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 9337, in 43 lists, size: 0.009 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p43g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181647
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  30726
 10  34756
 20  52
 30  2
min no. words: 0 at 6
max no. words: 21 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.621 Mbytes in 4 blocks
79076 words; after pruning: 75222
Sorting words ... Done

8  34810
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
.. Done
Total space allocated: 2.520 Mbytes; currently free: 0.883 Mbytes in 7 blocks
# pass words: 3351, #fail words: 5899
Quickalign: 12 successes, 31 failures
2678 SWAT alignments performed. 39 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.518 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.811 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.812 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.812 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2840, in 39 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p43g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181648
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  33235
 10  32279
 20  20
 30  2
min no. words: 0 at 6
max no. words: 21 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.682 Mbytes in 4 blocks
79076 words; after pruning: 62894
Sorting words ... Done

8  32301
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.712 Mbytes in 5 blocks
# pass words: 193, #fail words: 294
Quickalign: 0 successes, 0 failures
183 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.289 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.289 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.289 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.289 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p43g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181648
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  990166
 10  58410
min no. words: 0 at 1
max no. words: 7 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.280 Mbytes in 3 blocks
79076 words; after pruning: 62588
Sorting words ... Done

11  61304
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
... Done
Total space allocated: 6.048 Mbytes; currently free: 0.813 Mbytes in 7 blocks
# pass words: 3905, #fail words: 8266
Quickalign: 0 successes, 0 failures
3832 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 6 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.321 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p43g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181657
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  211846
 10  50296
 20  2
min no. words: 0 at 1
max no. words: 11 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.401 Mbytes in 3 blocks
79076 words; after pruning: 62792
Sorting words ... Done

9  50298
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
..... Done
Total space allocated: 2.520 Mbytes; currently free: 0.430 Mbytes in 5 blocks
# pass words: 5971, #fail words: 17240
Quickalign: 0 successes, 0 failures
5481 SWAT alignments performed. 0 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 4 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181701
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  211846
 10  50296
 20  2
min no. words: 0 at 1
max no. words: 11 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.401 Mbytes in 3 blocks
79076 words; after pruning: 62792
Sorting words ... Done

9  50298
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 0.430 Mbytes in 5 blocks
# pass words: 10674, #fail words: 0
Quickalign: 0 successes, 0 failures
287 SWAT alignments performed. 0 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 4 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181701
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  33235
 10  32279
 20  20
 30  2
min no. words: 0 at 6
max no. words: 21 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.682 Mbytes in 4 blocks
79076 words; after pruning: 62894
Sorting words ... Done

8  32301
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 1.216 Mbytes in 6 blocks
# pass words: 33492, #fail words: 0
Quickalign: 0 successes, 0 failures
930 SWAT alignments performed. 0 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 6 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.793 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181702
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Finding words ...
 0  2
 10  176
 20  66
 30  4
 40  28
 50  104
 60  94
 70  142
 80  114
 90  78
 100  80
 110  36
 120  34
 130  18
 140  6
 150  14
 160  12
 170  2
 180  4
 190  4
 220  4
 250  2
min no. words: 0 at 408
max no. words: 250 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.434 Mbytes in 3 blocks
79076 words; after pruning: 63200
Sorting words ... Done

5  1022
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
... Done
Total space allocated: 2.016 Mbytes; currently free: 0.705 Mbytes in 5 blocks
# pass words: 32588, #fail words: 0
Quickalign: 8 successes, 0 failures
3271 SWAT alignments performed. 8 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.025 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.823 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.823 Mbytes in 11 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.823 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 26, in 8 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181702
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  973089
 10  75285
 20  166
 30  32
 40  2
 140  2
min no. words: 0 at 6
max no. words: 138 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  75487
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
.1.008 Mbytes allocated -- total 8.064 Mbytes
..... Done
Total space allocated: 8.064 Mbytes; currently free: 2.283 Mbytes in 9 blocks
# pass words: 12276, #fail words: 0
Quickalign: 531 successes, 58 failures
6708 SWAT alignments performed. 589 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.885 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 8.064 Mbytes; currently free: 6.635 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.638 Mbytes in 11 blocks
Total space allocated: 8.064 Mbytes; currently free: 6.638 Mbytes in 11 blocks
Total # pairs: 2000, size: 0.088 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 9576, in 589 lists, size: 0.010 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181702
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.281 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.281 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  973255
 10  75133
 20  172
 30  12
 40  2
 140  2
min no. words: 0 at 6
max no. words: 137 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.611 Mbytes in 4 blocks
93032 words; after pruning: 92874
Sorting words ... Done

10  75321
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.
descrip_buffer expanded.1.008 Mbytes allocated -- total 7.560 Mbytes
 Done
Total space allocated: 7.560 Mbytes; currently free: 1.781 Mbytes in 9 blocks
# pass words: 4776, #fail words: 17773
Quickalign: 326 successes, 100 failures
2634 SWAT alignments performed. 403 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.415 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.167 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.169 Mbytes in 11 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.169 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 20421, in 403 lists, size: 0.020 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181703
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  979732
 10  68820
 20  22
 60  2
min no. words: 0 at 6
max no. words: 59 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.201 Mbytes in 3 blocks
78984 words; after pruning: 78366
Sorting words ... Done

10  68844
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.976 Mbytes in 10 blocks
# pass words: 988, #fail words: 9276
Quickalign: 13 successes, 2 failures
715 SWAT alignments performed. 10 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.561 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.343 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.343 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.343 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 739, in 10 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181703
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  979771
 10  68781
 20  22
 60  2
min no. words: 0 at 6
max no. words: 59 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.201 Mbytes in 3 blocks
78984 words; after pruning: 78306
Sorting words ... Done

11  74192
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
..0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.969 Mbytes in 8 blocks
# pass words: 2316, #fail words: 9354
Quickalign: 148 successes, 89 failures
2603 SWAT alignments performed. 223 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.542 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.323 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.324 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.324 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 10792, in 223 lists, size: 0.011 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181705
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  981706
 10  66848
 20  20
 40  1
 50  1
min no. words: 0 at 6
max no. words: 41 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.220 Mbytes in 3 blocks
76220 words; after pruning: 75366
Sorting words ... Done

11  71922
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 1.007 Mbytes in 9 blocks
# pass words: 641, #fail words: 2238
Quickalign: 5 successes, 97 failures
632 SWAT alignments performed. 69 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.565 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.352 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.352 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.352 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 12425, in 69 lists, size: 0.012 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181706
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  981878
 10  66676
 20  20
 50  2
min no. words: 0 at 6
max no. words: 41 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.221 Mbytes in 3 blocks
75960 words; after pruning: 75162
Sorting words ... Done

10  66698
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.552 Mbytes; currently free: 1.019 Mbytes in 11 blocks
# pass words: 476, #fail words: 7783
Quickalign: 32 successes, 0 failures
430 SWAT alignments performed. 17 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.588 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.376 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.376 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.376 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 594, in 17 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181706
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  208284
 10  53816
 20  42
 60  2
min no. words: 0 at 6
max no. words: 56 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.347 Mbytes in 3 blocks
75960 words; after pruning: 74316
Sorting words ... Done

9  53860
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes

descrip_buffer expanded Done
Total space allocated: 3.024 Mbytes; currently free: 0.641 Mbytes in 8 blocks
# pass words: 922, #fail words: 11505
Quickalign: 27 successes, 4 failures
939 SWAT alignments performed. 28 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.060 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.352 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.352 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.352 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 707, in 28 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181706
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  983186
 10  65368
 20  20
 40  2
min no. words: 0 at 6
max no. words: 40 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.230 Mbytes in 3 blocks
75960 words; after pruning: 73512
Sorting words ... Done

10  65390
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded....... Done
Total space allocated: 6.048 Mbytes; currently free: 0.516 Mbytes in 7 blocks
# pass words: 8101, #fail words: 31335
Quickalign: 21 successes, 18 failures
8018 SWAT alignments performed. 30 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.076 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.864 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.864 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.864 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1635, in 30 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181710
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  985996
 10  62558
 20  20
 40  2
min no. words: 0 at 6
max no. words: 38 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.247 Mbytes in 3 blocks
75960 words; after pruning: 70084
Sorting words ... Done

10  62580
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
...
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 1.029 Mbytes in 9 blocks
# pass words: 4586, #fail words: 17270
Quickalign: 25 successes, 167 failures
4448 SWAT alignments performed. 158 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.549 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.336 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.337 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.337 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 23037, in 158 lists, size: 0.023 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181713
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  35672
 10  29698
 20  159
 30  5
 90  2
min no. words: 0 at 22
max no. words: 82 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.187 Mbytes in 3 blocks
75960 words; after pruning: 62060
Sorting words ... Done

8  29864
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
. Done
Total space allocated: 2.520 Mbytes; currently free: 0.977 Mbytes in 8 blocks
# pass words: 2166, #fail words: 4910
Quickalign: 4 successes, 24 failures
1868 SWAT alignments performed. 18 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.548 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.848 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.848 Mbytes in 10 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.848 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1266, in 18 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181715
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  36940
 10  28449
 20  140
 30  5
 90  2
min no. words: 0 at 22
max no. words: 82 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.210 Mbytes in 3 blocks
75960 words; after pruning: 57530
Sorting words ... Done

8  28596
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.762 Mbytes in 6 blocks
# pass words: 138, #fail words: 243
Quickalign: 0 successes, 0 failures
134 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.312 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.312 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.312 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.312 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181715
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  996746
 10  51808
 20  20
 40  2
min no. words: 0 at 6
max no. words: 37 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.311 Mbytes in 3 blocks
75960 words; after pruning: 57208
Sorting words ... Done

11  54904
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
.. Done
Total space allocated: 6.552 Mbytes; currently free: 1.238 Mbytes in 8 blocks
# pass words: 2890, #fail words: 11397
Quickalign: 0 successes, 1 failures
2860 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.719 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.719 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.719 Mbytes in 7 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.719 Mbytes in 7 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181721
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  218160
 10  43948
 20  34
 60  2
min no. words: 0 at 6
max no. words: 53 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.432 Mbytes in 3 blocks
75960 words; after pruning: 57420
Sorting words ... Done

9  43984
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
.... Done
Total space allocated: 3.024 Mbytes; currently free: 0.716 Mbytes in 7 blocks
# pass words: 4846, #fail words: 22383
Quickalign: 0 successes, 2 failures
4550 SWAT alignments performed. 2 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.052 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.344 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.344 Mbytes in 8 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.344 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 218, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181725
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  218828
 10  43282
 20  32
 50  2
min no. words: 0 at 6
max no. words: 44 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.438 Mbytes in 3 blocks
75960 words; after pruning: 56272
Sorting words ... Done

9  43316
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
 Done
Total space allocated: 3.024 Mbytes; currently free: 0.733 Mbytes in 7 blocks
# pass words: 14605, #fail words: 0
Quickalign: 11 successes, 8 failures
334 SWAT alignments performed. 19 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.062 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.858 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.858 Mbytes in 8 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.858 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 632, in 19 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181725
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  37282
 10  28167
 20  81
 30  4
 80  2
min no. words: 0 at 22
max no. words: 72 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.221 Mbytes in 3 blocks
75960 words; after pruning: 55238
Sorting words ... Done

8  28254
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 1.019 Mbytes in 9 blocks
# pass words: 34905, #fail words: 0
Quickalign: 2 successes, 0 failures
858 SWAT alignments performed. 2 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.558 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.858 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.858 Mbytes in 11 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.858 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 41, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181725
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Finding words ...
 0  6
 10  228
 20  24
 30  44
 40  114
 50  108
 60  118
 70  102
 80  82
 90  54
 100  28
 110  20
 120  28
 130  12
 140  8
 150  14
 160  4
 170  4
 180  2
 190  4
 200  6
 220  4
 230  6
 260  2
 410  2
min no. words: 0 at 102
max no. words: 402 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.478 Mbytes in 3 blocks
75960 words; after pruning: 55302
Sorting words ... Done

5  1018
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
.. Done
Total space allocated: 1.512 Mbytes; currently free: 0.269 Mbytes in 6 blocks
# pass words: 41435, #fail words: 0
Quickalign: 20 successes, 10 failures
2203 SWAT alignments performed. 30 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.549 Mbytes in 5 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.353 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.353 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.353 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 118, in 30 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181725
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  972103
 10  76296
 20  164
 30  9
 40  1
 50  1
 120  2
min no. words: 0 at 14
max no. words: 111 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  76473
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
....1.008 Mbytes allocated -- total 8.064 Mbytes
. Done
Total space allocated: 8.064 Mbytes; currently free: 2.283 Mbytes in 9 blocks
# pass words: 10831, #fail words: 0
Quickalign: 342 successes, 0 failures
5531 SWAT alignments performed. 342 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.939 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 8.064 Mbytes; currently free: 6.691 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.692 Mbytes in 11 blocks
Total space allocated: 8.064 Mbytes; currently free: 6.692 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1511, in 342 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181725
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  972294
 10  76119
 20  152
 30  9
 120  2
min no. words: 0 at 5
max no. words: 111 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.610 Mbytes in 4 blocks
93148 words; after pruning: 92950
Sorting words ... Done

10  76282
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
..
descrip_buffer expanded Done
Total space allocated: 6.552 Mbytes; currently free: 0.772 Mbytes in 7 blocks
# pass words: 4718, #fail words: 14635
Quickalign: 362 successes, 134 failures
2764 SWAT alignments performed. 461 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.401 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.153 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.155 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.155 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 24393, in 461 lists, size: 0.024 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181726
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.305 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.305 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980705
 10  67864
 20  4
 30  3
min no. words: 0 at 5
max no. words: 26 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.216 Mbytes in 3 blocks
76636 words; after pruning: 75992
Sorting words ... Done

10  67871
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.505 Mbytes in 8 blocks
# pass words: 678, #fail words: 5020
Quickalign: 4 successes, 8 failures
509 SWAT alignments performed. 6 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.079 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.865 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.865 Mbytes in 7 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.865 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 326, in 6 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181726
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.305 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.305 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980752
 10  67817
 20  4
 30  3
min no. words: 0 at 5
max no. words: 26 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.217 Mbytes in 3 blocks
76636 words; after pruning: 75930
Sorting words ... Done

11  72880
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
.. Done
Total space allocated: 6.552 Mbytes; currently free: 1.002 Mbytes in 9 blocks
# pass words: 2229, #fail words: 7537
Quickalign: 95 successes, 85 failures
2406 SWAT alignments performed. 171 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.565 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.351 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.352 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.352 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 8341, in 171 lists, size: 0.008 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181728
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  982501
 10  66068
 20  4
 30  3
min no. words: 0 at 5
max no. words: 26 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.231 Mbytes in 3 blocks
74488 words; after pruning: 73672
Sorting words ... Done

11  70846
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
 Done
Total space allocated: 6.048 Mbytes; currently free: 0.527 Mbytes in 7 blocks
# pass words: 510, #fail words: 1970
Quickalign: 11 successes, 52 failures
544 SWAT alignments performed. 59 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.078 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.869 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.869 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.869 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 10814, in 59 lists, size: 0.011 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181729
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  983153
 10  65416
 20  4
 30  3
min no. words: 0 at 5
max no. words: 26 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.236 Mbytes in 3 blocks
73666 words; after pruning: 72882
Sorting words ... Done

10  65423
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.547 Mbytes in 8 blocks
# pass words: 581, #fail words: 4990
Quickalign: 32 successes, 23 failures
511 SWAT alignments performed. 48 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.102 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.895 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.895 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.895 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2986, in 48 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181729
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  209408
 10  52712
 20  20
 40  4
min no. words: 0 at 6
max no. words: 36 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.366 Mbytes in 3 blocks
73666 words; after pruning: 71228
Sorting words ... Done

9  52736
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes

descrip_buffer expanded Done
Total space allocated: 3.024 Mbytes; currently free: 0.677 Mbytes in 10 blocks
# pass words: 936, #fail words: 7675
Quickalign: 25 successes, 3 failures
956 SWAT alignments performed. 22 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.081 Mbytes in 10 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.377 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.377 Mbytes in 11 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.377 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 800, in 22 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181730
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  984936
 10  63633
 20  4
 30  3
min no. words: 0 at 5
max no. words: 26 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.248 Mbytes in 3 blocks
73666 words; after pruning: 70622
Sorting words ... Done

10  63640
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded....... Done
Total space allocated: 6.552 Mbytes; currently free: 1.055 Mbytes in 11 blocks
# pass words: 8327, #fail words: 27374
Quickalign: 35 successes, 28 failures
8257 SWAT alignments performed. 54 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.599 Mbytes in 11 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.392 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.392 Mbytes in 11 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.392 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2313, in 54 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181734
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  988776
 10  59793
 20  4
 30  3
min no. words: 0 at 5
max no. words: 26 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.271 Mbytes in 3 blocks
73666 words; after pruning: 66002
Sorting words ... Done

10  59800
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.0.504 Mbytes allocated -- total 6.552 Mbytes
..
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 1.070 Mbytes in 9 blocks
# pass words: 4147, #fail words: 15417
Quickalign: 8 successes, 81 failures
4056 SWAT alignments performed. 71 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.579 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.372 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.372 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.372 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 14379, in 71 lists, size: 0.014 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181736
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  36600
 10  28811
 20  110
 30  10
 50  2
 60  3
min no. words: 0 at 6
max no. words: 54 at 65280
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.207 Mbytes in 3 blocks
73666 words; after pruning: 58850
Sorting words ... Done

8  28936
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
. Done
Total space allocated: 2.016 Mbytes; currently free: 0.509 Mbytes in 7 blocks
# pass words: 2092, #fail words: 4581
Quickalign: 7 successes, 10 failures
1776 SWAT alignments performed. 15 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.065 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 936, in 15 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181738
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  37681
 10  27738
 20  102
 30  10
 50  2
 60  3
min no. words: 0 at 6
max no. words: 54 at 65280
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.227 Mbytes in 3 blocks
73666 words; after pruning: 54816
Sorting words ... Done

8  27855
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.299 Mbytes in 5 blocks
# pass words: 139, #fail words: 236
Quickalign: 0 successes, 0 failures
133 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.835 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 1.512 Mbytes; currently free: 0.835 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.835 Mbytes in 4 blocks
Total space allocated: 1.512 Mbytes; currently free: 0.835 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181738
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  998787
 10  49782
 20  4
 30  3
min no. words: 0 at 5
max no. words: 24 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.329 Mbytes in 3 blocks
73666 words; after pruning: 54420
Sorting words ... Done

11  52644
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
.. Done
Total space allocated: 6.552 Mbytes; currently free: 1.399 Mbytes in 7 blocks
# pass words: 2988, #fail words: 10010
Quickalign: 0 successes, 0 failures
2933 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.865 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.865 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.865 Mbytes in 6 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.865 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181744
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  219528
 10  42600
 20  12
 40  4
min no. words: 0 at 5
max no. words: 36 at 261120
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.449 Mbytes in 3 blocks
73666 words; after pruning: 54684
Sorting words ... Done

9  42616
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
.... Done
Total space allocated: 3.024 Mbytes; currently free: 0.751 Mbytes in 7 blocks
# pass words: 4741, #fail words: 20752
Quickalign: 0 successes, 3 failures
4394 SWAT alignments performed. 3 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.073 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 8 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 223, in 3 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181748
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  220038
 10  42090
 20  12
 40  4
min no. words: 0 at 5
max no. words: 36 at 261120
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.453 Mbytes in 3 blocks
73666 words; after pruning: 53860
Sorting words ... Done

9  42106
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
 Done
Total space allocated: 3.024 Mbytes; currently free: 0.764 Mbytes in 7 blocks
# pass words: 11925, #fail words: 0
Quickalign: 2 successes, 0 failures
295 SWAT alignments performed. 2 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.082 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.379 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.379 Mbytes in 7 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.379 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 15, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181748
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  37873
 10  27551
 20  101
 30  6
 50  2
 60  3
min no. words: 0 at 6
max no. words: 54 at 65280
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.231 Mbytes in 3 blocks
73666 words; after pruning: 53906
Sorting words ... Done

8  27663
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.542 Mbytes in 8 blocks
# pass words: 32838, #fail words: 0
Quickalign: 2 successes, 0 failures
902 SWAT alignments performed. 2 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.074 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.379 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.379 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.379 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 18, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181748
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.347 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.310 Mbytes in 2 blocks
Finding words ...
 0  16
 10  216
 20  32
 30  52
 40  118
 50  116
 60  100
 70  104
 80  80
 90  54
 100  30
 110  20
 120  26
 130  6
 140  4
 150  14
 160  6
 180  6
 190  4
 200  6
 230  6
 270  2
 280  4
 420  2
min no. words: 0 at 90
max no. words: 417 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.486 Mbytes in 3 blocks
73666 words; after pruning: 54240
Sorting words ... Done

5  1008
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
.. Done
Total space allocated: 2.016 Mbytes; currently free: 0.798 Mbytes in 8 blocks
# pass words: 40642, #fail words: 0
Quickalign: 33 successes, 0 failures
2197 SWAT alignments performed. 33 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.073 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.882 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.882 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.882 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 66, in 33 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181748
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  975164
 10  73130
 20  236
 30  38
 40  6
 260  2
min no. words: 0 at 6
max no. words: 258 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  73412
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.1.008 Mbytes allocated -- total 7.560 Mbytes
.... Done
Total space allocated: 7.560 Mbytes; currently free: 1.777 Mbytes in 7 blocks
# pass words: 13454, #fail words: 0
Quickalign: 474 successes, 29 failures
5885 SWAT alignments performed. 503 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.387 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.137 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.139 Mbytes in 8 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.139 Mbytes in 8 blocks
Total # pairs: 2000, size: 0.088 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2953, in 503 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181748
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  975310
 10  73004
 20  218
 30  36
 40  6
 260  2
min no. words: 0 at 6
max no. words: 254 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.609 Mbytes in 4 blocks
93274 words; after pruning: 93132
Sorting words ... Done

10  73266
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
..
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 0.770 Mbytes in 8 blocks
# pass words: 6430, #fail words: 26024
Quickalign: 425 successes, 172 failures
3622 SWAT alignments performed. 564 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.349 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.100 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.102 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.102 Mbytes in 8 blocks
Total # pairs: 2000, size: 0.088 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 30838, in 564 lists, size: 0.031 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181749
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.345 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.345 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  983057
 10  65495
 20  22
 130  2
min no. words: 0 at 6
max no. words: 128 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.225 Mbytes in 3 blocks
75276 words; after pruning: 74584
Sorting words ... Done

10  65519
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.552 Mbytes; currently free: 1.028 Mbytes in 8 blocks
# pass words: 1436, #fail words: 13639
Quickalign: 16 successes, 7 failures
929 SWAT alignments performed. 11 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.595 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.384 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.384 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.384 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 163, in 11 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181749
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.345 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.345 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  983106
 10  65446
 20  22
 130  2
min no. words: 0 at 6
max no. words: 128 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.225 Mbytes in 3 blocks
75276 words; after pruning: 74516
Sorting words ... Done

11  70256
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.. Done
Total space allocated: 6.048 Mbytes; currently free: 0.516 Mbytes in 6 blocks
# pass words: 2674, #fail words: 11374
Quickalign: 242 successes, 119 failures
2990 SWAT alignments performed. 352 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.065 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.853 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.855 Mbytes in 7 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.855 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 13865, in 352 lists, size: 0.014 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181752
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.311 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.311 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  985189
 10  63369
 20  16
 110  2
min no. words: 0 at 6
max no. words: 110 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.243 Mbytes in 3 blocks
72654 words; after pruning: 71730
Sorting words ... Done

11  67894
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 1.057 Mbytes in 8 blocks
# pass words: 473, #fail words: 2960
Quickalign: 12 successes, 63 failures
588 SWAT alignments performed. 49 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.605 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.399 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.399 Mbytes in 7 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.399 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 4788, in 49 lists, size: 0.005 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181752
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  985498
 10  63060
 20  16
 110  2
min no. words: 0 at 6
max no. words: 110 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.246 Mbytes in 3 blocks
72230 words; after pruning: 71348
Sorting words ... Done

10  63078
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes

descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 1.071 Mbytes in 9 blocks
# pass words: 1228, #fail words: 12153
Quickalign: 117 successes, 49 failures
1056 SWAT alignments performed. 116 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.617 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.412 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.413 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.413 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 4219, in 116 lists, size: 0.004 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181753
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  211836
 10  50268
 20  38
 80  2
min no. words: 0 at 6
max no. words: 71 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.385 Mbytes in 3 blocks
72230 words; after pruning: 67870
Sorting words ... Done

9  50308
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes

descrip_buffer expanded. Done
Total space allocated: 4.032 Mbytes; currently free: 1.715 Mbytes in 11 blocks
# pass words: 1013, #fail words: 12669
Quickalign: 70 successes, 64 failures
1161 SWAT alignments performed. 103 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 3.097 Mbytes in 12 blocks
Printing matches ...  Done
Total space allocated: 4.032 Mbytes; currently free: 2.892 Mbytes in 13 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.893 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.893 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 4097, in 103 lists, size: 0.004 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181753
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  989133
 10  59433
 20  8
 50  2
min no. words: 0 at 6
max no. words: 50 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.272 Mbytes in 3 blocks
72230 words; after pruning: 66184
Sorting words ... Done

10  59443
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded...... Done
Total space allocated: 6.048 Mbytes; currently free: 0.585 Mbytes in 9 blocks
# pass words: 7594, #fail words: 28135
Quickalign: 29 successes, 10 failures
7512 SWAT alignments performed. 36 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.108 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.904 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.904 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.904 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1643, in 36 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181756
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  992497
 10  56069
 20  8
 50  2
min no. words: 0 at 6
max no. words: 50 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.291 Mbytes in 3 blocks
72230 words; after pruning: 62424
Sorting words ... Done

10  56079
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
...
descrip_buffer expanded. Done
Total space allocated: 6.048 Mbytes; currently free: 0.597 Mbytes in 8 blocks
# pass words: 4026, #fail words: 16076
Quickalign: 63 successes, 99 failures
4201 SWAT alignments performed. 144 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.096 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.890 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.891 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.891 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 6156, in 144 lists, size: 0.006 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181759
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  37564
 10  27851
 20  102
 30  17
 80  2
min no. words: 0 at 6
max no. words: 73 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.219 Mbytes in 3 blocks
72230 words; after pruning: 56832
Sorting words ... Done

8  27972
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
. Done
Total space allocated: 2.016 Mbytes; currently free: 0.532 Mbytes in 7 blocks
# pass words: 2048, #fail words: 4325
Quickalign: 10 successes, 11 failures
1761 SWAT alignments performed. 18 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.078 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.385 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.385 Mbytes in 9 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.385 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 993, in 18 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181800
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  38607
 10  26816
 20  96
 30  15
 80  2
min no. words: 0 at 6
max no. words: 71 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.238 Mbytes in 3 blocks
72230 words; after pruning: 52984
Sorting words ... Done

8  26929
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.310 Mbytes in 5 blocks
# pass words: 124, #fail words: 240
Quickalign: 0 successes, 0 failures
119 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.837 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 1.512 Mbytes; currently free: 0.837 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.837 Mbytes in 4 blocks
Total space allocated: 1.512 Mbytes; currently free: 0.837 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181800
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  1000630
 10  47936
 20  8
 40  2
min no. words: 0 at 6
max no. words: 34 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.340 Mbytes in 3 blocks
72230 words; after pruning: 52556
Sorting words ... Done

11  50674
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.. Done
Total space allocated: 6.048 Mbytes; currently free: 0.915 Mbytes in 6 blocks
# pass words: 2902, #fail words: 10043
Quickalign: 0 successes, 0 failures
2863 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.372 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.372 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.372 Mbytes in 5 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.372 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181806
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  221176
 10  40944
 20  22
 50  2
min no. words: 0 at 6
max no. words: 48 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.460 Mbytes in 3 blocks
72230 words; after pruning: 52840
Sorting words ... Done

9  40968
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
.... Done
Total space allocated: 3.024 Mbytes; currently free: 0.773 Mbytes in 7 blocks
# pass words: 4438, #fail words: 20258
Quickalign: 0 successes, 2 failures
4159 SWAT alignments performed. 2 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.086 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.385 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.385 Mbytes in 8 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.385 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 132, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181810
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  221528
 10  40594
 20  20
 50  2
min no. words: 0 at 6
max no. words: 48 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.464 Mbytes in 3 blocks
72230 words; after pruning: 52156
Sorting words ... Done

9  40616
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 0.282 Mbytes in 6 blocks
# pass words: 11767, #fail words: 0
Quickalign: 10 successes, 1 failures
288 SWAT alignments performed. 11 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.591 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.394 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.394 Mbytes in 8 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.394 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 122, in 11 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181810
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  38790
 10  26663
 20  72
 30  9
 60  2
min no. words: 0 at 6
max no. words: 56 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.245 Mbytes in 3 blocks
72230 words; after pruning: 51644
Sorting words ... Done

8  26746
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.820 Mbytes in 6 blocks
# pass words: 31467, #fail words: 0
Quickalign: 0 successes, 0 failures
820 SWAT alignments performed. 0 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.340 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.340 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.340 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.340 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181810
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.348 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.312 Mbytes in 2 blocks
Finding words ...
 0  12
 10  226
 20  26
 30  60
 40  130
 50  112
 60  120
 70  100
 80  60
 90  50
 100  32
 110  14
 120  18
 130  12
 140  12
 150  6
 160  8
 170  2
 180  2
 190  8
 200  2
 210  2
 220  4
 260  4
 410  2
min no. words: 0 at 102
max no. words: 406 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.499 Mbytes in 3 blocks
72230 words; after pruning: 52094
Sorting words ... Done

5  1012
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
.. Done
Total space allocated: 1.512 Mbytes; currently free: 0.318 Mbytes in 6 blocks
# pass words: 40778, #fail words: 0
Quickalign: 97 successes, 0 failures
2295 SWAT alignments performed. 97 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.581 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.392 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.393 Mbytes in 11 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.393 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 208, in 97 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181810
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.283 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.283 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  975803
 10  72473
 20  252
 30  36
 40  10
 160  2
min no. words: 0 at 6
max no. words: 151 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.619 Mbytes in 4 blocks
91660 words; after pruning: 91642
Sorting words ... Done

10  72773
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
.... Done
Total space allocated: 7.056 Mbytes; currently free: 1.301 Mbytes in 7 blocks
# pass words: 10590, #fail words: 0
Quickalign: 146 successes, 0 failures
4413 SWAT alignments performed. 146 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.951 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.707 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.708 Mbytes in 9 blocks
Total space allocated: 7.056 Mbytes; currently free: 5.708 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 801, in 146 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181811
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.283 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.283 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  975897
 10  72385
 20  246
 30  36
 40  10
 160  2
min no. words: 0 at 6
max no. words: 151 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.621 Mbytes in 4 blocks
91450 words; after pruning: 91372
Sorting words ... Done

10  72679
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
..
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 0.795 Mbytes in 7 blocks
# pass words: 6384, #fail words: 19070
Quickalign: 471 successes, 148 failures
3531 SWAT alignments performed. 587 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.364 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.119 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.121 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.121 Mbytes in 9 blocks
Total # pairs: 2000, size: 0.088 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 31749, in 587 lists, size: 0.032 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181811
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.349 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.349 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.314 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.314 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  985726
 10  62842
 20  6
 40  2
min no. words: 0 at 6
max no. words: 34 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.255 Mbytes in 3 blocks
70724 words; after pruning: 70034
Sorting words ... Done

10  62850
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.588 Mbytes in 8 blocks
# pass words: 755, #fail words: 6733
Quickalign: 2 successes, 3 failures
559 SWAT alignments performed. 3 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.132 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.930 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.930 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.930 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 195, in 3 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181811
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.349 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.349 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.314 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.314 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  985776
 10  62792
 20  6
 40  2
min no. words: 0 at 6
max no. words: 34 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.255 Mbytes in 3 blocks
70724 words; after pruning: 69966
Sorting words ... Done

11  67250
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
.. Done
Total space allocated: 6.552 Mbytes; currently free: 1.087 Mbytes in 7 blocks
# pass words: 2091, #fail words: 7065
Quickalign: 92 successes, 79 failures
2256 SWAT alignments performed. 164 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.621 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.419 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.419 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.419 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 8356, in 164 lists, size: 0.008 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181813
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.352 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.352 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.317 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.317 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  987599
 10  60969
 20  6
 40  2
min no. words: 0 at 6
max no. words: 33 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.270 Mbytes in 3 blocks
68602 words; after pruning: 67756
Sorting words ... Done

11  65226
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 1.113 Mbytes in 8 blocks
# pass words: 910, #fail words: 2025
Quickalign: 17 successes, 108 failures
784 SWAT alignments performed. 125 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.623 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.426 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.426 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.426 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 21648, in 125 lists, size: 0.022 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p39g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181814
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  988448
 10  60120
 20  6
 40  2
min no. words: 0 at 6
max no. words: 33 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.276 Mbytes in 3 blocks
67568 words; after pruning: 66758
Sorting words ... Done

10  60128
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.552 Mbytes; currently free: 1.136 Mbytes in 9 blocks
# pass words: 670, #fail words: 6190
Quickalign: 44 successes, 5 failures
579 SWAT alignments performed. 41 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.663 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.467 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.468 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.468 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1365, in 41 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181815
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  213672
 10  48448
 20  22
 50  2
min no. words: 0 at 6
max no. words: 47 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.407 Mbytes in 3 blocks
67568 words; after pruning: 64886
Sorting words ... Done

9  48472
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes

descrip_buffer expanded Done
Total space allocated: 3.024 Mbytes; currently free: 0.763 Mbytes in 7 blocks
# pass words: 706, #fail words: 9705
Quickalign: 19 successes, 1 failures
729 SWAT alignments performed. 18 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.136 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.444 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.444 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.444 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 700, in 18 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181815
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  990320
 10  58248
 20  6
 40  2
min no. words: 0 at 6
max no. words: 33 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.288 Mbytes in 3 blocks
67568 words; after pruning: 64360
Sorting words ... Done

10  58256
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded...... Done
Total space allocated: 6.048 Mbytes; currently free: 0.637 Mbytes in 8 blocks
# pass words: 7253, #fail words: 26084
Quickalign: 4 successes, 17 failures
7163 SWAT alignments performed. 20 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.151 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.956 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.956 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.956 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1706, in 20 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181818
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  992230
 10  56338
 20  6
 40  2
min no. words: 0 at 6
max no. words: 33 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.299 Mbytes in 3 blocks
67568 words; after pruning: 62178
Sorting words ... Done

10  56346
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
...
descrip_buffer expanded. Done
Total space allocated: 6.048 Mbytes; currently free: 0.640 Mbytes in 8 blocks
# pass words: 4485, #fail words: 14525
Quickalign: 7 successes, 159 failures
4151 SWAT alignments performed. 163 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.112 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.916 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.917 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.917 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 31377, in 163 lists, size: 0.031 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181821
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Finding words ...
 0  38360
 10  27088
 20  83
 30  2
 40  1
 50  2
min no. words: 0 at 6
max no. words: 48 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.244 Mbytes in 3 blocks
67568 words; after pruning: 53188
Sorting words ... Done

8  27176
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
. Done
Total space allocated: 2.016 Mbytes; currently free: 0.593 Mbytes in 6 blocks
# pass words: 1925, #fail words: 3928
Quickalign: 10 successes, 15 failures
1645 SWAT alignments performed. 23 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.119 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.436 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.436 Mbytes in 9 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.436 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1350, in 23 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181822
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Finding words ...
 0  39792
 10  25666
 20  73
 30  2
 40  1
 50  2
min no. words: 0 at 6
max no. words: 48 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.266 Mbytes in 3 blocks
67568 words; after pruning: 48806
Sorting words ... Done

8  25744
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.369 Mbytes in 4 blocks
# pass words: 149, #fail words: 233
Quickalign: 0 successes, 0 failures
145 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.875 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 1.512 Mbytes; currently free: 0.875 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.875 Mbytes in 4 blocks
Total space allocated: 1.512 Mbytes; currently free: 0.875 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p39g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181822
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  1003880
 10  44688
 20  8
min no. words: 0 at 6
max no. words: 20 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.368 Mbytes in 3 blocks
67568 words; after pruning: 48416
Sorting words ... Done

11  47054
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.. Done
Total space allocated: 6.048 Mbytes; currently free: 0.971 Mbytes in 7 blocks
# pass words: 2670, #fail words: 8801
Quickalign: 0 successes, 0 failures
2624 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.407 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.407 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.407 Mbytes in 6 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.407 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p39g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181828
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  223698
 10  38426
 20  18
 40  2
min no. words: 0 at 6
max no. words: 32 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.488 Mbytes in 3 blocks
67568 words; after pruning: 48676
Sorting words ... Done

9  38446
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
... Done
Total space allocated: 2.520 Mbytes; currently free: 0.587 Mbytes in 5 blocks
# pass words: 4148, #fail words: 18144
Quickalign: 0 successes, 0 failures
3855 SWAT alignments performed. 0 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 4 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181831
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  223698
 10  38426
 20  18
 40  2
min no. words: 0 at 6
max no. words: 32 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.488 Mbytes in 3 blocks
67568 words; after pruning: 48676
Sorting words ... Done

9  38446
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 0.587 Mbytes in 5 blocks
# pass words: 10410, #fail words: 0
Quickalign: 0 successes, 0 failures
226 SWAT alignments performed. 0 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 4 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.879 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181831
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Finding words ...
 0  39792
 10  25666
 20  73
 30  2
 40  1
 50  2
min no. words: 0 at 6
max no. words: 48 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.266 Mbytes in 3 blocks
67568 words; after pruning: 48806
Sorting words ... Done

8  25744
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.623 Mbytes in 7 blocks
# pass words: 27044, #fail words: 0
Quickalign: 1 successes, 0 failures
691 SWAT alignments performed. 1 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.129 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.950 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.950 Mbytes in 11 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.950 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 17, in 1 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:181831
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.353 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_26157.ThuMar9181603CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.319 Mbytes in 2 blocks
Finding words ...
 0  28
 10  210
 20  30
 30  90
 40  134
 50  118
 60  114
 70  78
 80  70
 90  38
 100  22
 110  22
 120  16
 130  12
 140  2
 150  8
 160  2
 170  10
 180  2
 190  4
 200  4
 220  2
 260  6
 340  2
min no. words: 0 at 101
max no. words: 337 at 0
avg no. words: 0.0 Done
Total space allocated: 0.504 Mbytes; currently free: 0.018 Mbytes in 2 blocks
67568 words; after pruning: 49072
Sorting words ... Done

5  996
Finding subject matches ...0.504 Mbytes allocated -- total 1.008 Mbytes
0.504 Mbytes allocated -- total 1.512 Mbytes
. Done
Total space allocated: 1.512 Mbytes; currently free: 0.375 Mbytes in 6 blocks
# pass words: 40182, #fail words: 0
Quickalign: 86 successes, 0 failures
1877 SWAT alignments performed. 86 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.623 Mbytes in 5 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.444 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.444 Mbytes in 9 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.444 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 217, in 86 lists, size: 0.000 Mbytes